Eating Kerogen

Black sludge, eventually turning into kerogen, that forms at the bottom of a pond or lake is created from anaerobic bacteria.Credit: NSTA

When microorganisms die in ponds of water or in the ocean, they slowly sink to the bottom, forming a thick black sludge. Over time, this sludge becomes buried and compacted by more organisms and layers of mud. If oxygen is left out of the mixture, the organic matter can’t decay and it eventually fossilizes into the material called kerogen.

Scientists have long believed that kerogen was a carbon sink — a place where carbon was trapped and could not be recycled. But recently, a team of researchers led by Steven Petsch of the Woods Hole Oceanographic Institution (WHOI) discovered that microorganisms in Kentucky’s New Albany Shale are eating kerogen.

The scientists cultured the bacteria from the 370-million-year-old black shale. The New Albany Shale formed during the Devonian (417 to 354 million years ago), when Kentucky was covered by shallow tropical seas. Kerogen is plentiful in the Kentucky shales because the ancient waters were very fertile, with lots of microorganisms like algae and planktonic bacteria at the surface, while the ocean bottom was stagnant, with limited dissolved oxygen.

The scientists know the bacteria are consuming the kerogen, because they designed their experiment so that kerogen was the only source of carbon available for the bacteria to eat.

The scientists also tested the abundance of carbon-14 (C-14) in the bacteria. Living organisms gather small amounts of radioactive C-14 from their environment. When organisms die, they no longer accumulate C-14. Over time, the C-14 decays away. Because kerogen is composed of organic matter, it initially contains the C-14 accumulated by the dead organisms. But because the New Albany Shale is so old, the C-14 has completely decayed. The kerogen in the shale no longer contains any C-14.

"We grew bacteria collected from this rock and measured the C-14 content of their cells," says Petsch. "These measurements showed that these living bacteria contain very little to no C-14. The only way that living organisms can contain no C-14 is to live in an environment where all of the available carbon is also C-14 free."

Kerogen was thought to be resistant to bacterial consumption before this discovery. While most of the organic materials in algae and bacteria – such as the proteins, nucleic acids and carbohydrates – are usually degraded or consumed very quickly after a cell dies, the materials that eventually form kerogen are not as easily degraded or eaten by other organisms. These materials accumulate in sediments, lasting for millions of years. The composition of this fossilized material tends to be very resistant to chemical or biological attack.

Algae, bacteria, spores and cuticle link and form dark specks of kerogen.Credit: UKOOA

"In composition, the kerogen in New Albany Shale is somewhat similar to many common plastics like polyethylene," says Petsch. "Think of plastic baggies. We know that most plastics persist a long time in the environment."

This discovery indicates that microorganisms may play a more active role in the Earth’s carbon cycle than previously recognized. Specifically, this bacterial feasting may play a significant role in recycling the carbon in kerogen. At the present time, however, the scientists don’t know how prevalent are the bacteria, or how much carbon they consume.

"We don’t know if these organisms occur in many environments, or are just special to this outcrop in Kentucky," says Petsch. "We don’t even know yet how abundant they are in that environment, because we grew them in the lab. And so far, we have no way to estimate how much carbon they are consuming in Kentucky."

According to Petsch, exposure to the atmosphere seems to play some sort of role in the degradation of the kerogen.

"The rock closest to the surface at our exposure in Kentucky has lost a lot of kerogen," says Petsch. "At ten feet down into the hillside, the rock contains about ten percent kerogen, while at the surface, the rock has about one percent. Perhaps these organisms are responsible for all of this loss."

Petsch thinks perhaps that the bacteria need oxygen in order to consume the kerogen. While the shale exposed to the atmosphere had less kerogen, the deeper rock had limited oxygen exposure and thus less bacterial activity.

"Consumption of the shale most likely does depend on exposure environment," says Petsch. "In the deep subsurface, oxygen could not penetrate from air into the rock. Our work seems to indicate that availability of oxygen plays some role in how kerogen is consumed. So at depth, microbial activity should be very limited."

Petsch doesn’t think what happened in the New Albany ocean was just a local occurrence. This study could therefore tell us something about the abundance of carbon dioxide in the Earth’s atmosphere over geological time.

Tiny single celled plant life called phytoplankton absorb carbon dioxide from the atmosphere and nutrient rich waters and grow in wide colonies called blooms.Credit: NASA/GSFC

"Massive burial of organic matter was occurring in many places around the globe at this time in earth’s history," says Petsch. "To bury all of this carbon, you need to have a very large population of phytoplankton (algae and bacteria). Some researchers believe that this global event may have resulted in a lowering of carbon dioxide in the earth’s atmosphere because the growth and burial of so many photosynthetic organisms was effectively removal of carbon from the atmosphere to seafloor sediments."

"I think the discovery of this microbial process is important scientifically," says Linda Jahnke, a bacteriologist with the NASA Ames Research Center. "There is a growing appreciation of microbially-mediated geological processes today. The fact that bacteria can live almost anywhere and make a living from the most meager means certainly broadens our concept of the potential for life in extreme and extraterrestrial environments."

What Next?

Petsch and his team are planning to go back to Kentucky to obtain a much longer core sample into the rock. He also hopes to determine how widespread the bacteria may be in other shale environments.

In addition, Petsch plans to conduct several different types of analyses on the kerogen-eating bacteria.

"I want to figure out what these organisms are, through DNA sequencing and phylogenetic analysis," says Petsch. "I’d also like to work on specifically how these organisms attack the kerogen, by looking at the step-wise chemical reactions involved."